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Sample GSM1480369 Query DataSets for GSM1480369
Status Public on Feb 04, 2015
Title RNAPII ChIP-seq TNF Rep2
Sample type SRA
 
Source name adipocyte_RNAPII ChIP-seq TNF
Organism Homo sapiens
Characteristics cell type: SGBS adipocyte D10
treated with: 10ng/ml TNFα for 90min
chip antibody: RNAPII
chip antibody vendor: Diagenode
chip antibody cat. #: C15200004
Treatment protocol Mature SGBS adipocyte D10 were treated with 10ng/ml TNFα or vehicle for 90 min before harvest of total RNA or chromatin.
Growth protocol SGBS cells were grown to confluence in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 Ham’s supplemented with 10% fetal bovine serum, 33 µM biotin, 17 µM pantothenate, 100 µg/ml streptomycin, 62.5 µg/ml penicillin, 1ng/µl fibroblast growth factors (FGF) 1, and 90 µg/µl heparin. At two days postconfluency, SGBS cells were stimulated to differentiate with serum-free growth medium supplemented with 10 nM insulin, 200 pM triiodothyronine, 1 µM cortisol, 2 µM BRL 49653, 0.115 mg/ml MIX, 0.25 mmol/L DEX, and 0.01 mg/ml human transferrin. After 3 days, the medium was replaced with the differentiation medium without FGF1 and heparin, and after 6 days Rosiglitazone/BRL49653, MIX, and DEX was removed from the medium.
Extracted molecule genomic DNA
Extraction protocol ChIP experiments were performed according to standard protocol as described in (Siersbæk et al. 2012, MCB, 32: 3452-3463)
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Description processed data file: RNAPII_Gene_counts.txt
Data processing alignment: ChIP-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) specifying --alignIntronMax 1 to avoid potentially aligning across exon-exon junctions.
quantification: RNAPII ChIP-seq coverage within gene bodies were quantified using the iRNA-seq pipeline (Madsen et al, Submitted). The first 500 bp of the gene were omitted to avoid quantifying stalled RNAPII
Genome_build: hg19
 
Submission date Aug 17, 2014
Last update date May 15, 2019
Contact name Susanne Mandrup
E-mail(s) s.mandrup@bmb.sdu.dk
Phone +45 6550 2340
Organization name University of Southern Denmark
Department Biochemistry and Molecular Biology
Street address Campusvej 55
City Odense M
ZIP/Postal code 5230
Country Denmark
 
Platform ID GPL18460
Series (1)
GSE60462 iRNA-seq: Computational method for genome wide assessment of acute transcriptional regulation from total RNA-seq data
Relations
BioSample SAMN02996449
SRA SRX682086

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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